Qiaomu Hu

The tomato hind (Cephalopholis sonnerati) is an emerging mariculture species increasingly threatened by Vibrio harveyi infection, yet in vitro tools for studying its immune defense remain limited. Here, we established a novel fin-derived fibroblast-like cell line, designated Tomato hind Grouper Fin (TGF), from C. sonnerati using the tissue explant method. TGF cells have been stably subcultured for more than 83 passages in Leibovitz’s L-15 medium supplemented with 20% fetal bovine serum at 28 °C. Species authentication via mt-co1 barcoding confirmed 99.9% sequence identity, and karyotype analysis revealed a diploid chromosome number of 2n = 48, matching the donor species. TGF cells exhibited robust post-thaw viability (>80%) and were amenable to exogenous nucleic acid delivery, with higher efficiency for siRNA than plasmid DNA. To evaluate immune competence, TGF cells were challenged with V. harveyi, and transcriptomic profiling was performed at 60, 90, and 120 min post-infection. A total of 1876 differentially expressed genes were identified at 120 min. KEGG enrichment analysis revealed sustained activation of Toll-like receptor, NOD-like receptor, NF-κB, TNF, and IL-17 signaling pathways across all time points. The TGF cell line represents a valuable in vitro resource for studying host–pathogen interactions of C. sonnerati.

Extrachromosomal circular DNA (eccDNA) serves as a vital regulator of gene expression and phenotypic plasticity. The Monopterus albus is a protogynous hermaphroditic fish, and the functional role of eccDNA during its female-to-male sex reversal remains poorly understood. We conducted Circle-seq analysis on gonadal tissues of super-female and male individuals and integrated our findings with previously published gonadal RNA-seq data. A total of 62,574 and 34,562 eccDNAs were, on average, identified in the two groups, and 7881 down-regulated and 2738 up-regulated differentially abundant eccDNAs were screened in male gonads. Three candidate eccDNAs, eccDNA^Dmrt1a, eccDNA^Sox9a1 and eccDNA^ZNF239, were selected for subsequent analysis. Quantitative real-time PCR was applied to detect the overall transcriptional levels of their corresponding host genes, covering transcripts derived from both genomic DNA and eccDNA. Spatiotemporal expression profiling and letrozole induction experiments revealed male-biased expression of Dmrt1a and Sox9a1, while ZNF239 was predominantly expressed in female gonads. Complete sex reversal was observed in female M. albus after 90-day letrozole treatment, accompanied by elevated Dmrt1a/Sox9a1 and reduced ZNF239 transcription. Fluorescence in situ hybridization localized these transcripts in gonadal germ cells and somatic cells across developmental stages. This study verifies the production of eccDNA during gonadal development. The results indicate that Dmrt1a and Sox9a1 may facilitate sex reversal and suggest that ZNF239 is likely involved in ovarian development. This work provides novel clues for deciphering the molecular mechanism underlying sex reversal from the eccDNA perspective.

The rapid expansion of aquaculture breeding has increased the need to identify wild genetic resources for germplasm management and sustainable breeding. However, distinguishing wild from domesticated populations remains challenging in species with recent domestication histories and low genetic differentiation. In this study, we used the large yellow croaker (Larimichthys crocea) as a case study species to develop specific insertion/deletion (InDels)-based identification methods for wild and domesticated populations based on whole-genome resequencing data. Four large-fragment InDels with significant allelic frequency differences between populations were selected as one marker panel. In addition, four coding-region InDels predicted to alter amino acid sequences were selected as another marker panel based on allele-frequency differences, coding-region annotation, and supporting SNP-based Fst or nucleotide-diversity signals. Principal component analysis (PCA) based on these selected InDel loci showed partial separation with some overlap between wild and domesticated samples. Therefore, multi-locus scoring models were established by assigning scores to wild-predominant alleles. Receiver operating characteristic (ROC) analysis showed strong discriminatory performance for both panels, with area under the ROC curve (AUC) values of 0.9608 and 0.9771 and classification agreement rates with known sample status of 90.0% and 91.7%, respectively. These results indicate that targeted InDel markers can provide a practical PCR-based approach for distinguishing wild and domesticated large yellow croaker populations with limited genetic differentiation. This workflow may provide a reference for marker development in other recently domesticated species, although further validation in independent populations and target species is needed.

Fish represent the most species-rich group within the phylum Chordata, possessing exceptional nutritional and ornamental value. Global aquaculture, particularly finfish farming, is experiencing rapid expansion worldwide, and fish serve as crucial model organisms for vertebrate developmental biology and functional genomics research. However, traditional breeding methods are plagued by limitations such as low precision and lengthy breeding cycles. Currently, gene editing technologies represented by the CRISPR/Cas system, base editing, and prime editing have provided revolutionary tools for dissecting gene function, modeling human diseases, targeted trait improvement, and ecological adaptation studies. This review describes the evolutionary history of gene editing technology, compares gene delivery strategies in fish embryos, and highlights landmark applications in key areas, including gene function research, aquaculture breeding, ornamental fish coloration regulation, and human disease model construction. Finally, we propose that innovation should be pursued while ensuring biosafety and regulatory compliance, to promote the transformation of fish gene editing toward large-scale and safe application.

The Qinghai–Tibet Plateau and surrounding mountain regions form one of the world’s most distinctive freshwater environmental gradients. Schizothoracinae are among the most representative endemic fish lineages in these systems and provide a useful model for studying how drainage history, genome evolution, adaptation, and conservation interact. In this review, we synthesize schizothoracine research within an environment–evolution–conservation framework. We examine how drainage history and connectivity shape divergence and gene exchange, how polyploidy and genome remodeling provide the genomic background for adaptive inference, and how phenotypic and population-genomic evidence can be translated into conservation units and management priorities. Across current studies, cold-associated metabolic remodeling and UV-related DNA damage response and repair emerge as the most recurrent molecular themes, whereas hypoxia-related signals are more context-dependent. We further show that morphology, otolith chemistry, age–growth traits, and population structure can strengthen MU/ESU interpretation when integrated with genomic evidence. Future progress will depend on broader chromosome-level genome coverage, more systematic comparison of structural genomic variation, standardized stressor-linked designs, and denser sampling in geomorphic transition zones and putative hybrid regions.

The Qinghai–Tibet Plateau and surrounding montane valleys comprise one of the world’s most pronounced freshwater environmental gradients, where cold, intense UV radiation, variable dissolved oxygen, and heterogeneous hydrodynamics interact with drainage reorganization and connectivity constraints. Schizothoracinae are among the most representative endemic lineages in these systems, combining exceptional lineage diversity with pervasive polyploid genomic backgrounds. Here we synthesize schizothoracine research through an “environment–evolution–conservation” framework, linking (i) taxonomic and phylogenetic foundations under pervasive convergence, cryptic diversity, and hybridization; (ii) geologic history and drainage evolution as drivers of radiation and gene exchange; (iii) polyploidy, post-WGD structural remodeling, and early rediploidization as a testable process rather than a static ploidy fact; and (iv) omics resources and analytical pipelines that enable verifiable evidence chains across comparative genomics, population genomics, and tissue-level stress responses. Across major stressors, recurrent molecular themes emerge for cold-associated metabolic remodeling and UV-associated DNA repair and genome maintenance, whereas hypoxia-related signals are often inconsistent, plausibly reflecting strong spatiotemporal heterogeneity and multi-route physiological accommodation. We further connect molecular candidates to functional outcomes using reusable phenotypic evidence streams, including geometric morphometrics, high-throughput phenotyping, otolith microchemistry, and age–growth life-history syndromes of slow growth and longevity. Finally, we translate population structure into operational MU/ESU delineation and propose an auditable, iterative management checklist centered on MU-aligned stocking, connectivity performance metrics during critical seasonal windows, and quantified habitat restoration targets. We conclude by outlining priorities to raise evidentiary strength across basins: chromosome-level genomes across lineages, systematic SV/TE comparisons, standardized stressor–phenotype–transcriptome designs, and intensified sampling in geomorphic transition zones and putative hybrid regions to enable cumulative, decision-ready synthesis.

Hemibagrus guttatus is a commercially valuable freshwater fish in the Pearl River Basin, renowned as the “King of Freshwater Fish.” Due to habitat degradation and overfishing, its wild population has declined sharply, leading to its listing as a National Key Protected Wild Animal of Class II in China. Artificial breeding is therefore crucial for conservation, yet progress is hindered by the lack of clear sexual dimorphism and poor understanding of its sex differentiation mechanism. In this study, we performed high-throughput RNA sequencing (RNA-seq) to compare gonadal transcriptomes of male and female H. guttatus. A total of 3245 differentially expressed genes (DEGs) were identified, including 3122 male-biased and 123 female-biased DEGs, which clustered into three distinct expression patterns. Enrichment analysis revealed that genes associated with the TGF-β (Transforming Growth Factor-beta) and GnRH (Gonadotropin-Releasing Hormone) signaling pathways were significantly enriched in the female gonads, suggesting their potential roles in gonadal differentiation. From the DEG set, we further highlighted five genes with pronounced sex-biased expression: rbm46 (RNA Binding Motif Protein 46) exhibited gonad-specific expression, whereas myc (v-myc avian myelocytomatosis viral oncogene homolog), angptl4 (Angiopoietin-Like 4), sox9 (SRY-Related HMG-Box Gene 9), and fzd2 (Frizzled Class Receptor 2) showed marked expression differences between male and female gonads. These findings provide insights into the molecular mechanisms underlying sex differentiation in H. guttatus, offer potential molecular markers for sex identification, and establish a scientific basis for germplasm conservation and the optimization of breeding techniques.

Nr5a2 (nuclear receptor subfamily 5, group a, member 2) is involved in gonad development and sex hormone synthesis. In this study, the full length of Nr5a2f and Nr5a2m were obtained by Nr5a2 variable splicing from Andrias davidianus, and the tissue distribution was detected. We identified Nr5a2f of 2455 bp and Nr5a2m of 2150 bp length, encoding 479 and 325 amino, respectively. We first characterized Nr5a2f and Nr5a2m gene expression in developing gonads. Results showed that Nr5a2f had significantly high expression in the ovary and little expression in other tissues, during the sex differentiation and sex reversal, Nr5a2f expression was gradually decreased in the ovary and the expression in the testis was significantly lower than in the ovary from 1 year to 6 year old. Significantly high expression was observed in the ovary and reversal ovary, while low expression was in the testis and reversal testis. While Nr5a2m expression exhibited the opposite profile, high expression was observed in the brain and testis. During sex differentiation and sex reversal, high expression was shown in the testis and low expression in the ovary from one year to six years old and significantly higher expression emerged in testis and reversal testis than in ovary and reversal ovary. In situ hybridization, results showed that Nr5a2f began to express in female undifferentiated gonads and the expression level increased from 48 dpf to 91, while Nr5a2m was expressed in male undifferentiated gonads. Three RNA interference sites were designed and we detected that site 293 exhibited a significant inhibitory effect in ovary cells. After Nr5a2f expression was inhibited by site 293, we observed that female-based gene Nr5a2f, foxl2 and cyp19 expression were decreased, while the male-based gene dmrt1 and cyp17 expression was increased. These results suggested that Nr5a2f and Nr5a2m exhibited different expression patterns in the process of sex differentiation, which provided a foundation for further functional characterizations.